KO Gene Cluster Analysis: comparison of wild type and Delta-yap1 strains
A bioinformatic tool was developed (see Materials and Methods) to infer gene network organization from perturbed expression profiles.
Two sets of microarray expression data corresponding to the time course effects of benomyl on gene expression of wild type and yap1D were compared.
(A) Typical graphs corresponding to different time points represent, for each gene significantly up-regulated in the wild type strain,
log2(Ratio) values for wild type (X) and yap1D (Y) strains.
(B) A hierarchical clustering analysis could be carried out from the two sets of data (see Materials and Methods). The resulting tree was split
into five groups I, II, III, IV, and V. Clusters I, II, III and IV were enlarged in order to display complete gene lists. For each gene,
their expression profiles in the wild type and yap1D time course experiments are represented using the common color code
(green : repressed and red : induced). (D) Only subsets of genes were extracted from the cluster V (see the supplemental data for the complete list).
Those genes correspond to pertinent functional categories : REDOX CONTROL, REGULATION and PROTEIN FOLDING, which distinguish the benomyl response.
Systematic search for the regulatory motifs of the transcription factor Yap1 (TTANTAA), Pdr1/Pdr3 (TCCGYGGA) and STRE (AGGGG) was performed in the
up-stream sequence of all this genes. In C, mean differential expression profiles for clusters I, II, III, IV and V are represented.
The mean values were calculated for each time point and the standard deviation is represented as a grey line along the two X and Y axes.
|
